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Fixed calculations for Mark 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1330 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-29 03:21:43 +00:00
parent f0378db9b7
commit 72dda0b85c
1 changed files with 8 additions and 5 deletions
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13
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java
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@ -89,17 +89,20 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
public List<String> done() {
List<String> s = new ArrayList<String>();
s.add(String.format("name %s", dbName));
s.add(String.format("\t\tCALLED_REF\tCALLED_VAR_HET\tCALLED_VAR_HOM\tNO_CALL\t\t\tTOTALS\tDISCOVERY_ACCURACY\tGENOTYPE_ACCURACY"));
s.add(String.format("\t\tCALLED_REF\tCALLED_VAR_HET\tCALLED_VAR_HOM\tNO_CALL\t\t\tTOTALS\tTRUE_GENOTYPE_CONCORDANCE\tGENOTYPE_SENSITIVITY"));
for (int i=0; i < 4; i++) {
StringBuffer sb = new StringBuffer();
sb.append(TRUTH_NAMES[i] + "\t");
for (int j=0; j < 4; j++)
sb.append(table[i][j] +" (" + cellPercent(table[i][j], truth_totals[i]) + ")\t\t");
sb.append(truth_totals[i]);
if ( i == TRUTH_VAR_HET || i == TRUTH_VAR_HOM )
sb.append("\t"+cellPercent(table[i][CALL_VAR_HET]+table[i][CALL_VAR_HOM], truth_totals[i]) + "\t\t\t" + cellPercent(table[i][i], truth_totals[i]));
if ( i == TRUTH_VAR_HET || i == TRUTH_VAR_HOM ) {
sb.append("\t"+cellPercent(table[i][i], table[i][CALL_REF]+table[i][CALL_VAR_HET]+table[i][CALL_VAR_HOM]) + "\t\t\t");
sb.append(cellPercent(truth_totals[i]-table[i][NO_CALL], truth_totals[i]));
}
s.add(sb.toString());
}
s.add("VARIANT_SENSITIVITY: " + cellPercent(table[TRUTH_VAR_HET][CALL_VAR_HET]+table[TRUTH_VAR_HET][CALL_VAR_HOM]+table[TRUTH_VAR_HOM][CALL_VAR_HET]+table[TRUTH_VAR_HOM][CALL_VAR_HOM], truth_totals[TRUTH_VAR_HET]+truth_totals[TRUTH_VAR_HOM]));
s.add("\n");
s.add(String.format("\t\tCALLED_REF\tCALLED_VAR_HET\tCALLED_VAR_HOM\tNO_CALL"));
for (int i=0; i < 4; i++) {
@ -118,8 +121,8 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
s.add(TRUTH_NAMES[i]+"_"+CALL_NAMES[j]+"_PERCENT_OF_CALLS "+cellPercent(table[i][j], calls_totals[j]));
}
if ( i == TRUTH_VAR_HET || i == TRUTH_VAR_HOM ) {
s.add(TRUTH_NAMES[i]+"_DISCOVERY_ACCURACY "+cellPercent(table[i][CALL_VAR_HET]+table[i][CALL_VAR_HOM], truth_totals[i]));
s.add(TRUTH_NAMES[i]+"_GENOTYPE_ACCURACY "+cellPercent(table[i][i], truth_totals[i]));
s.add(TRUTH_NAMES[i]+"_TRUE_GENOTYPE_CONCORDANCE "+cellPercent(table[i][i], table[i][CALL_REF]+table[i][CALL_VAR_HET]+table[i][CALL_VAR_HOM]));
s.add(TRUTH_NAMES[i]+"_GENOTYPE_SENSITIVITY "+cellPercent(truth_totals[i]-table[i][NO_CALL], truth_totals[i]));
} }
return s;
}